We are left with a few cues which are not included in the film, some of which have been mentioned earlier in this list.  For the sake of completion, a full list in included here:

From the SONY CD:
Track 4       0:00-1:08 (Jar Jar music)
Track 11    1:23-1:38 (Probe Droid alt)
Track 12    0:55-1:11 (Duel of the Fates material)
Track 14    3:20-3:45 (Spooky synth music)

From the PHANTOM MENACE video game CD-ROM:
Sqassaultintro.imc: this is some action music using the ostinato motif from “Duel of the Fates”

Sqfederation.imc:  this version of “Activating the Battledroids” contains extra moments not in the movie or the OST

Sqfight5.imc:  unused action music.  There is some controversy as to where this music fits in with Williams original conception.  It appears on the OST in edited form between music for "The Invasion Begins" and "The Bongo (part 3)".  Some feel it is music for when "Qui-Gon Rescues Jar Jar", a sequence that may have been longer when Williams scored the picture, and may have included a deleted scene of Obi-Wan Kenobi rising from underwater in the swamps of Naboo (this can be viewed in a CGI cut-scene in the TPM CD-ROM game.)  I now think it belongs somewhere in THE BATTLE OF NABOO

Sqfightmaul2.imc:  this is an alternate, film version of a portion of “Duel of the Fates”.  It is most likely "6m4 - The Great Dual" (sic), the recording of which can be seen in Part 12 of Lynne's Diary at www.starwars.com

Sqfightmaul2end.imc:   this is an unused cadence

Sqgripping2.imc: this is additional music for marching Battledroids.  It has been theorized by Jim Ware that this piece was intended to score the "Ascension Guns" section of the movie

Sqmaulduelstart.imc:  this is an unused recording of the choir intro in “Duel of the Fates”

Sqplayerdeath.imc:   this is an unused cadence

Sqreactor.imc:  this file is an alternate mix of the opening measures of "Anakin Destroys The Federation Ship".

Sqscary2.imc:   this is a low string swell (possibly a remix of “Darth Maul Arrives on Tatooine”)

From the RACER video game CD-ROM:
“ConflictLoop” consists of an instrumental mix of a minute or so of “Duel of the Fates”.  No choir. (This was not recorded for inclusion in the film, in my opinion)

"ConflictLoop2" contains an alternate version/mix of about a minute or so of "Duel of the Fates". (concert arrangement, again not intended for use in the film, in my opinion)

From the JEDI POWER BATTLES CD for Playstation:
Track 4a contains the most complete version available of John William's original conception of "THE HANGAR BATTLE".  It actually segues directly into file 5b mentioned below.  None of this music appears in the film as it is presented here, and much of it doesn't appear at all.

Track 5a is a complete presentation of "Jedi Fight", which contains music not heard in the UE and an alternate mix of the opening measures. Also available, in inferior sound quality, on TPM CD-ROM as sqdroidfightloop.imc

Track 5b contains about 30 seconds of music based on the Trade Federation theme which does not appear in the film.

Track 06j features the alternate version of "The Gungun March" .  It features stronger percussion and some synth-sounding tuba/trombone music.  This cue is also heard on TPM CD-ROM in sqfederation.imc in lower sound quality.